The Last of Us: Independence
by ConanPeinTLOU
Summary: This story starts off right as the game is ending. It explores both Joel and Ellie's feelings and insights on their situation. They'll experience the hardships of surviving in a world ravished by epidemic. This story will explore the coming years Joel and Ellie will have together... and the years they will spend apart. This isn't a Joel/Ellie love story. First fanfic! Enjoy!
1. Chapter 1

The Last of Us: Independence

**(Authors Note): Okay so I'm just going to start off by saying this is my first fan fiction story, ever. I want to be a writer, specifically for video games. I thought that maybe this would be a good outlet to test my skills and grow as a writer. I am extremely open to suggestions and constructive criticism. For this story, I will not be making this purely for people who want a love story or something that is not The Last of Us. I will try as hard as I can to keep the characters as true to the game as I can. This story will be based on what I perceive as the story as soon as the game ends. There will likely be no time skip, no "two years later" kind of thing. This will be the kind of story that I would love to see Naughty Dog make again. A story that made me cry, laugh, yell in anger, and fear. Honestly, I would love if people accepted this and loved the story, but for all intents and purposes, this story is really for me. Like I said, I love The Last of Us and have played through the main campaign many times. No story has touched me in such a way as this. Naughty Dog truly made a masterpiece that will be my favorite game and story for years to come. So with that, let's begin.**

She stared at me. I couldn't determine her feelings at the moment. The way she looked at me broke my heart. She knew I was lying to her, I could tell, which made it that much harder not to just come out and say that I damned the human race because of selfish reasons. Over the past year I had grown to love Ellie as my own daughter. I had traveled across the entire country, fought hunters, runners, clickers, and bloaters to get her to the fireflies.

I took on this task as an obligation, at first, because of Tess. She and I had a complicated work relationship and I felt I owed it to her to carry this little girl across the country, to potentially save people from meeting the same fate as Tess. But as we continued on our "adventure," my reasoning became something of a far cry from what it originally was. I grew to really care about this little girl. Hell, I grew to love this girl as my own daughter. I didn't see her as replacing Sarah. No one could ever replace her. But Ellie brought something completely new into my life that had been absent since I lost Sarah. A reason to live. Something to fight for.

"Swear to me… Swear to me that everything you said about the Fireflies is true."

When she spoke those words to me, everything went quiet. The forest was no longer bustling with wildlife. The sound of the small waterfall faded into nothingness. She stared at me, waiting for my answer.

"… I swear."

She looked at me, obviously gathering her thoughts.

"Okay."

I knew she didn't believe me because she restrained herself from squeezing more information out of me. It was very unlike her. It was unsettling.

"Thank you, Joel."

My eyes widened slightly, "For what, Ellie?"

"For everything," she responded, and started walking past me down the hill to Tommy's. "Come on, Joel! It's past lunch and I'm starving!" I jogged up beside her and looked down at her. I was unsure if my lie would change how our relationship would remain and grow. She saw me looking and smiled up at me. That simple gesture, that tiny display of emotion let me know that she understood why I did what I did, at least a little bit. While she would have undoubtedly given her life for this shithole of a world, she would have done the same for me.

My thoughts drifted as we walked, getting closer and closer to Tommy's. I didn't regret anything I did for that little girl. The only thing I regret was not getting to her in time before she was forced to kill that animal she called David. It visibly left her emotionally scarred from that experience, and I wince every time I think about what could have happened if she hadn't grabbed that machete, or if I hadn't been close by. That experience changed her, and I hate myself for not getting to her sooner.

"Stop right there or I'll put a bullet right between your eyes!" yelled a young man, maybe only a few years older than Ellie, in one of the many guard towers surrounding the town.

"Listen son, I'm a friend of Tommy's. If you could tell him we've come back, I'd really appreciate it."

"I'm not doing shit! How do I know you're not a hunter or-"

"Will, put the gun down. He's a friend," spoke a familiar voice from behind the opening gates. "I was starting to think you'd never come back." He patted me on the shoulder. "You look like you've gained a few years in the last few months."

I chuckled, "Yeah, well, there's a reason for that, little brother. A topic of conversation for another time, I'm afraid. He looked at me for a moment and then turned to greet Ellie. They did their little exchange with Tommy making a joke and Ellie coming back with a little jab. "You still got room for us in this town of yours?" I asked.

"I think we can find a hole for you to crawl in."

**Okay so I know it wasn't very long but I just kind of wanted to set up the theme, I guess, for this story. I will dive into more emotional waters in the next chapter and address some of the reasons why Joel did what he did to save Ellie. Again, I appreciate any constructive criticisms anyone might have for me. I want this to be a gripping story so readers input is appreciated. I'll have another, longer chapter up in about two days most likely so stay tuned!**


	2. Chapter 2

Chapter 2

Shortly after Ellie and I arrived at Tommy's, we were greeted by a few familiar faces. A few of the men who were working on getting the power plant up and running the last time we visited were walking the streets, headed to their lookout duties. There were several children a few years younger than Ellie running around playing tag, nowhere near to the fences though. Ever since Tommy's people got the electricity going again, the fences have been pulsing with it. Many signs were erected to keep the children away because the fence was meant to kill the infected, not scare them.

We met up with Maria about ten minutes after our arrival. She hugged Ellie and nodded towards me with a grin on her face. As we were headed to wherever Tommy was taking us, I took in more of our surroundings. They had really cleaned the place up. Trash wasn't lying everywhere, green overgrowth had been cut and piled behind a few of the houses, and blood stains from previous skirmishes had been simply painted over so the children wouldn't ask about them. It was overall a nice change from the dirty environment I had gotten used to over the years. It brought back memories of the ranch Tommy and I tracked Ellie to. It seemed almost untouched by time, save a few boarded up windows and broken asphalt.

Tommy was also unusually jovial. Of course, we hadn't seen each other in years, and the last time we did, we nearly got in a fight, so it was nice to see my little brother enjoying life, no matter how shitty it was. Tommy and Maria were talking our ears off about how much progress they had made in the months since we had been gone, and honestly, I just wanted to lie down and get some rest. The stress from the last few days had taken its toll on me, Ellie too.

"Well, brother, here ya go. The place is yours. I know you like your privacy so the only neighbors you've got right now are Maria and me," Tommy spoke with our shared southern accent. I smiled and hugged him.

"Thanks, little brother. You have no idea what this means to us."

"Yea, especially me. I'm tired of sleeping on the ground and having to hear this old geezer sucking air all night," Ellie complained. We all laughed. It was moments like this that made me glad I didn't let that firefly walk me out of that hospital. I don't know what I would've done without Ellie.

"Well, guys, the sun's right over our heads right now so it's probably a little after noon. Everyone meets for supper in the basement of the power plant when the sun touches the horizon," Tommy said, talking to Ellie and I.

"Awesome! I'm already looking forward to it!" I was as excited as Ellie to have the opportunity to eat with good people for once, but I was looking forward more to sleep than food at the moment. Tommy and Maria said their goodbyes and headed toward their home a couple of houses down. I looked at Ellie, gave her a "C'mon, kiddo," and headed inside. It was a small house with two bedrooms. The living room had a couch and a loveseat, both next to the window overlooking the street. I dropped my backpack on the floor and fell onto the couch. Like I told Ellie in the forest, I was starting to feel my age. Ellie found her place on the loveseat and soon enough we were both in a dead slumber.

The basement of the power plant was a little larger and more put together than I thought. I expected it to be like a cold dungeon with stone walls, but instead it had about 8 long tables put together to make one long table. To get our food we had to stand in line and scoop the food from old pots and pans. The whole set up reminded me of when the outbreak hit and I had to stay in a shelter. They would line us up and feed us this way, but the difference between Tommy's and a shelter was that Tommy's was quickly beginning to feel like a home.

Back in Boston, people would stand for hours in the cold, heat, and rain to get what little food they could with ration cards and while Tommy's didn't have an abundance of food, everyone got the chance to eat. The food was delicious and the company was comforting. I had been used to isolating myself from the outside, but I could foresee that I would be unable to continue that twenty year long tradition I practiced, even if I wanted to.

Ellie and I sat next to Tommy and Maria, and during supper we were introduced to the town. We were pretty well received by everyone, considering that Ellie had stolen a horse and had gotten another one killed. After we ate the people approached us, shook our hands and made small talk. All of this was starting to feel like the old world, and it was nice. After a while the townspeople started heading to their homes to get ready for the next day. Ellie and I walked over to Maria and Tommy.

"Hey, baby brother. I was wondering if we could have a little chat."

"Sure, Joel. Maria, honey, would you mind taking Ellie home?" Tommy asked. "Me and the old man over here are gonna do a little catching up."

"Sure, sweetie. C'mon, Ellie," Maria said. Ellie looked at me for a moment then nodded and left with Maria. I looked at the door they exited through long after they left.

"What happened, Joel?" Tommy asked. I looked at the ground. My throat was starting to get dry and I was beginning to sweat.

"I killed 'em, Tommy," I confessed.

"What?"

"I killed them. The fireflies. I killed the soldiers, the doctors… I killed Marlene." I looked Tommy in the eyes and saw confusion.

"Why? What happened, Joel?" I told Tommy everything. Every single detail of what happened. From the time we arrived at the God forsaken hospital, to shooting that first soldier, to killing the rest, and then Marlene. I told him about how I lied to Ellie and how it's the only thing that I regret. I told him that I didn't regret killing the fireflies to save Ellie, and that if I had to do it again I would.

Tommy just watched me while I told him what happened. When I finished, he looked at the ground, sighed, and looked back at me.

"Listen, Joel. I was smart enough to figure out that you did something pretty drastic to get Ellie back here without having bullet holes in either of you. I was with the fireflies a long time, I know how they work and I know how the infection operates and spreads. I knew the only way to get a cure would be to remove it from the brain but I didn't know they would have to kill her. Honestly, I would have done the same thing for you, Maria, and Ellie. While I don't know her that well yet, I know that you care about her and that'd be all the reasonin' I'd need, big brother. And if anymore fireflies ever found you, you can bet that we'd be right by your side, everyone'd be," he said with a smile.

"That means a lot, Tommy. I also appreciate you takin' us in like you have. Hell, I'm in your debt." He laughed.

"Don't mention it. You can pay off that debt by goin' huntin' with me and Will tomorrow. Oh, and forgive him for the whole 'bullet between your eyes' thing. He was just doing his job."

"It's fine, and I'd be glad to join you two."

When Tommy and I said goodnight, I was expecting to walk into the house and see Sarah sleeping on the couch. I opened the door and instead saw a little red-haired girl in Sarah's place. I was then brought back to reality, but I wasn't sad like I thought I'd be. Ellie became my daughter, and I cared deeply for her. She gave me a reason to keep on living.

I closed the front door and turned to see Ellie waking up.

"Hey, Joel. You guys were gone for a while. What did you talk about?"

"We were just catching up. Talking about the stuff that happened since we left last fall."

"Well by the looks of things, they've gotten a lot of shit done," she said with her potty mouth that I'd gotten used to. "I mean, they've been to nearby towns that haven't been touched since the outbreak happened so they were about get tons of food and supplies."

"That reminds me, Ellie, I'm gonna go huntin' with Tommy and Will tomorrow morning. We should be back a few hours before supper. In the mean time, Maria is going to show you around the town and get you acquainted with the lookout guards 'cause you're gonna be playing border patrol."

"Awesome! I'm so glad you guys didn't stick me with some job like canned food counter or the cleaning lady."

We woke up early that morning to a knock on the door. My instinct and old habits had me rushing to my pistol, but when I remembered I was supposed to go hunting with Tommy, I put the gun back in my bag.

"Rise and shine big brother!" Tommy yelled. "It's time to go get us some meat!"

"Jesus, boy, keep it down. Can't you see I just woke up?"

"Oh don't be grumpy, Joel, huntin' is always fun around these parts. There's an abundance of wild game and the infected hardly ever show up around here 'cause we're so deep in the wilderness."

"Yeah I hear you. Just gimme' a second to get my gear and then we'll head out."

I woke up Ellie and told her to meet Maria at her house to eat breakfast and get ready for work. Tommy led me out of the house and towards the gates Ellie and I entered through when got here. That boy, Will, was already at the gates waiting for us. As soon as he saw me he ran up and apologized profusely. I told him everything would be alright as long as he didn't make that mistake again and gave him a friendly slap on the shoulder.

We opened and closed the gates and headed toward the mountains overlooking the town. This place truly was beautiful, and if the way Tommy talked about it was true, I could see Ellie and me settling here for quite a while.

**AN: Well, guys, I hope you enjoyed this chapter. Next chapter will be up in a couple of days. I put two up today because I thought the first chapter had been put up 3 days ago, but apparently it wasn't. So I decided I'd go ahead and write the second one. I made it a lot longer but next week I'll try to lengthen it a bit more because I know that writing this took me like an hour and a half but reading it will only take a few minutes I'm sure. Anyways, hope you enjoyed! **


	3. Chapter 3

Chapter 3

"Well, buddy, you're gonna have to shoot her in the head."

We had been walking for quite a while before Tommy told us to stop. He decided we needed a break, but it was pretty obvious he was doing it for me. We were at the base of a mountain. The air was chilled with humidity and the grass was still wet from the morning dew. We had walked deep into the woods and the trek up the base of the mountain had been more than a little strenuous. While we weren't rock climbing by any means, we still were walking up a pretty steep incline and I was starting to get tired. Once again, my age was making itself known. However, I tried my best to keep up with Tommy, who in turn, tried his best to keep up with Will.

"Hey, Tommy, how much farther until we get to this little valley of yours?" I asked. I was starting to get irritated. We'd been walking all morning and had yet to see this 'abundance of game' Tommy had been talking about so excitedly.

"We'll be there soon old geezer. Believe me, when you see this place, you'll be glad I brought us out all this way," Tommy said. We finally stopped in a small clearing surrounded by huge trees. "Well, we're here old man." I looked at him, looked at the opening in the trees, and then back at him.

"This is it?" I raised my voice, more than a little pissed that he would bring us out to this dinky little area. "Why the hell would we come all the way out here for this shit?!"

Tommy laughed, "Calm down, Joel. The real place is behind this." Tommy walked over to a part of the mountain that had a thick layer of green overgrowth draped in front of it. He pulled some of the greenery to the side, revealing a hidden cave. He motioned for us to go inside. We entered and he let the greenery fall back into its natural position. I looked back at Tommy as we started to walk. He gave me a prideful grin and a wink. I chuckled and continued through the cave with Will leading us.

"I'm guessing you've brought that boy here a couple of times, huh?"

"No," Tommy said, "He actually brought me here a couple of months ago. He was raised in the mountains here. He only found us because he had lost his entire family. His brother had been killed by a bear during a hunting accident, and his mother and father died from infection, but not the infection you're thinking. They were cut by some thorn bushes and didn't have anything to sterilize the cuts with."

"Damn," I looked toward Will who was walking ahead of us, oblivious to our conversation.

"Yeah. When he told us what happened, it was kind of hard to believe. Nowadays you hear about people getting killed by the infected or hunters. You sort of forget there are other ways to die too."

"Or you get killed by the military," I added, thinking back to Sarah once again. We were quiet the rest of the walk through the cave. Our flashlights were on in order to bring some light to the darkness enveloping the cave. We rounded a corner and immediately were greeted with tiny specks of light peeking out of what looked like more shrubbery hanging in front of an exit. We turned our lights off as Will pulled the overhang of green apart, allowing light to pour in.

We walked out onto a cliff overlooking a beautiful valley. This type of beauty had been absent from my world for over twenty years. Dirt and grime were what I was used to, but seeing this beautiful landscape, pulsing with the wild game that Tommy had mentioned, gave me hope that this shithole of a world wouldn't ruin this amazing place as well. Next to the cave entrance was a small path leading down into the valley. I followed Tommy down the path, preparing myself to carry whatever we killed all the way back to the town. That was the only thing that didn't excite me about this whole situation. I laughed slightly at myself and jogged to catch up to Tommy.

Joel woke me up and told me to go Maria's in a few minutes, and that he would be back home later today. I got my stuff together and headed out the door. Remembering where Maria's was, I walked down the cracked asphalt street to her home. During the walk, I pondered over what my job as 'border patrol' guard, as Joel called it, would entail. Surely being a lookout in a place like this wouldn't see much action, so I was hoping Maria would give me a few more responsibilities.

I walked up the wooden stairs to the porch and knocked on the door. Maria greeted me and invited me in. I took in my surroundings and noticed this place was a lot more 'home-y' feeling than the house Joel and I stayed in. Curtains, although a little raggedy, hung from the windows, furniture filled the living room and kitchen, and pictures of Tommy and Maria's family before the infection covered the walls. I thought of asking about what happened to her, Tommy, and Joel's family, but decided against it. It was much too early to be getting emotional and depressed.

"Come sit with me in the kitchen, hun. I made us breakfast," she offered. I wasn't expecting much, but I was surprised to see canned bacon and some fruit on the table, dumped onto old plates. It was a little odd seeing this since I never really sat at a table to eat other than the night before. I was really used to just eating on the ground next to a fire, or eating out of a tinfoil wrapping at the military academy where I used to live. It was a nice change of pace.

"Thanks, Maria. I'm starving."

"After all the food you ate last night? How in the world could you be hungry after that meal?" My face turned red and I pushed my plate toward her. "Oh, honey, I'm only kidding. Everyone is like that, especially after all the time you and Joel spent out in the wilderness. I'm sure there wasn't much to eat at all." I just nodded at her as I stuffed my face. She was right, there was hardly ever enough to eat. I had grown up living that way, though, so it wasn't that odd to me. I was used to it.

We finished breakfast and headed outside. Maria led me towards the power plant, and at first I thought she was going to tell me she wanted me to help prepare dinner. Instead we went down a street, and then down a small alley next to a house. We found ourselves in the backyard of this little house and my curiosity got the best of me.

"You don't want me to babysit kids or anything do you?" I asked. She chuckled softly.

"No, Ellie. We came here to get you ready for your lookout duties." She walked over to a cellar door on the ground next to the back porch. She pulled a key ring out of her pocket, fiddled with the lock on the door, and then lifted one of the doors up. She motioned for me to enter while she held the door above her head. I stepped down through the doors and walked down the stairs. She dropped the door behind me with a loud 'thud' and followed behind me. It was now so dark I couldn't see my hand in front of my face.

"Just a second," Maria said. I could hear her hands rubbing against the walls, as if she was searching for something. I heard the flip of a switch and the lights flickered on.

"How are there lights on right now?" I asked. "I don't hear a generator."

"Power plant, remember? With the guys utilizing the power from the hydroelectric dam and the power plant, we're able to keep the lights on all the time. We still cut the lights off at night though. If every house in town was lit up at night, we would probably be unknowingly attracting infected and hunters. Of course, we might be far enough away that we wouldn't have to worry about it, but we still don't want to take any chances." That made sense. She kept rambling on about how everything worked, getting all scientific on me. I didn't really care about any of that, though, so I sort of just tuned her out.

We walked down a hallway and came to a door where Maria had to use her keys again. She unlocked the door and guided me inside. The room was full of crates and cabinets. Maria walked over to one of the crates, opened it and pulled out a rifle. I then realized we were in the towns little armory. She told me to go over to one of the cabinets and get some ammo for my pistol. I opened one of the doors and took in just how much ammo they had.

These cabinets were old, wardrobe cabinets. So they were as tall as I was, a few were taller, and filled with ammunition. They must've either stumbled upon this, or looted a ton of abandoned towns to get all of these resources. I wanted to look around more but Maria was already heading out. I grabbed a couple boxes of bullets and followed her out. When we emerged back out into the back yard, Maria closed and locked the door behind. I made a reminder to myself to come check this out one night after Joel went to sleep.

We made our way through town, passing a few familiar faces from supper the night before, saying hi, and continuing on our way. We found ourselves at one of the lookout towers next to the fence. It wasn't really a tower so much as it was a box on an empty house.

"Alright, Ellie, Joel says you're a pretty good shot with a gun. He also says that you don't do well with jobs like cleaning or cooking. So we've decided to let you be one of our lookouts. Every morning around this time, our night shift lookouts will be getting off. So every day you'll go to that house we went to earlier, pick up a rifle and some ammo, and come here. You'll be up there until supper, which is when the night shift guys will come and take your place." She handed me a spare key to the 'armory' and started walking away.

"Wait. Maria," I called after her. "So I just stand here all day until something pops up?"

"Pretty much," she called back. "Oh, and if you see anything suspicious, run over to that little blue house on the corner. There's an old guy in there named Tyson. He'll come check it out." I nodded and turned to look at the lookout nest.

"I think tomorrow I'm gonna pack some comic books." I sighed and climbed up the ladder to start my first day as 'border patrol.'

"Shh. Joel, you see her?" Tommy asked. I nodded looking through my scope.

"Yeah, I see her. But I feel like we could get a little closer. Plus, that boy has been killing squirrel and rabbit all day with that bow he's got. I think he should take a shot at that deer. It would be quieter too," I commented. Tommy nodded in agreement with me. He slowly crept over to Will who was crouched up on a branch, in a tree next to us. Tommy told him the plan, and Will gave me a thumbs up. Tommy crawled back over to me and told me Will was ready. We all slowly made our way toward the creature grazing in the field, taking each step as slowly and as quietly as possible.

We finally got close enough so Will could take a shot. We were right on the tree line. The deer had looked in our direction a couple of times, thanks to the branch cracking underneath my boot, but we went relatively unnoticed. Will stood up, pulled the drawstring back, and just before he was ready to shoot, a gunshot cracked in the distance. The noise startled the deer, causing her to run away. Will followed the deer with his bow all the way to the edge of the field, then let an arrow fly.

We couldn't tell if Will hit her or not, but, at the moment, we were more concerned where that shot come from, and who fired it.

"Where the hell did that come from? I thought you said there was no one around these parts, Tommy?" I asked. The first thing I thought of, though, were the remaining fireflies I was unable to kill at the hospital.

"There isn't anyone else around here," Will retorted. "Whoever fired that shot must be either passing through, or hunting like us.

"Yeah, Joel. They probably won't cause us any harm, but I think it would be best if we steered clear of them. Just in case," added Tommy. I simply nodded, and we carried on with our hunt to look for blood from the deer Will shot at. Tommy and I walked to the spot where the deer had been when Will took a shot. We came up on a large pool of blood, waved at Will to come join us at the tree line, and then followed the blood stains into the forest.

Blood was everywhere. On the side of trees, on the ground covering the leaves, on bushes, but we'd yet to see a body. There were places on the ground where the leaves looked like they had been moved around and dirt had been kicked up. This was from the deer falling to the ground and kicking around, trying to get back up. Branches were broken and bushes were knocked over. There wasn't a whole lot of tracking involved. It was pretty evident that we would find a body pretty soon.

We pushed our way through thick, blood covered shrubs, and came into another clearing, where we discovered the stag. She was laying in the middle of the field with an arrow sticking out of the side of her stomach. As we got closer, we could tell the deer was struggling to breath. We had to make this quick, though. We had been out all day and supper would be in a couple hours. In the time we had before supper, we needed to kill the deer, skin her, put her in bags, and hike our way back to the town.

We approached the dying animal and saw her look up at us. She didn't even try to escape. She knew it was the end of the line. We waited for her to die for a few minutes, but she kept on breathing.

"Well, buddy, you're gonna have to shoot her in the head," Tommy said. Will nodded, pulled back an arrow, and released, sending an arrow into the dying creature's skull, ending her pain. Will yanked both of his arrows out of the deer and put them back in their quiver. Tommy pulled a long, sharp skinning knife out of his back pack. Before he could be skinning the deer, however, another shot boomed in the distance. Only this time, it was closer. Much, much closer.

**AN: Oooo, suspense. I'll have the next chapter up in a couple of days. Thanks to the people who have read the last two chapters. I intend for this story to be a long one. I've been trying to set up the plot and while it's taking a little while, it'll be worth it. I'm definitely writing a story that is interesting to me, so I hope the rest of the people who read this feel the same. Anyway, stay tuned for chapter four in the next few days. Thanks!**


End file.
